Currently only works on Linux or Mac OS X. Some configuration is needed for Windows compatability
- Python 3.4 or higher
- an sh-compatible shell (bash works just fine)
- IDLE (if working on widnows)
We are submitting three unique programs that simplify and improve the process of protein analysis for organisms across various domains of life. These tools are useful not only for our wet lab research, but for any projects incorporating proteins from different organisms. Firstly, the sequenceAnalysis.py program allows for quick, large scale protein analysis to provide an efficient filtering process for identifying proteins of interest. Secondly, the CodonBiasGenerator.py produces a GCG codon bias table of an organism for the process of codon optimization. Finally, the Frequency Optimized Codon Usage Strategy (FOCUS.py) tool is a working prototype that allows for the detection of rare codons based on an organism’s codon bias. This tool provides a novel method for codon optimization with respect to rare codons, which may improve protein production without loss of enzymatic function.
User guides are located in the User_Guides folder
There is no setup required to run any of the python programs. The only setup needed is to install Python 3.4 on your machine
FOCUS.py is a working prototype and is not finished. A new scoring method needs to be created to reduce the amount of noise for detecting rare codons.
The MIT License (MIT)
Copyright (c) 2015 igemsoftware
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.